I think this is the first thread I've started here, so it's a shame it's derivative of two topics of which this is only an important sub-topic. If this opening post is too long for you, focus on the red conclusions, then work your way back to the premises you disagree with, don't understand, or have a comment on--if you agree with the premises, but disagree with a conclusion, then explain how you think the argument is invalid. I will frequently post supporting links [#] without referring to their content; I don't suggest reading them all unless the claim they're nearby interests you, because there are going to be a lot.

Please focus on criticizing these reasons, not arguing alternatives like Intelligent Design or talking about tangents like abiogenesis and metaphysics. I ask just because this topic is important enough to stand alone.

P1-0) The same phenomenon under the same observed conditions is usually caused by the same process in the world.
* This is the basic premise of empirical inductive reasoning, and is a key to the scientific method in general.P2-0) Theories explain a phenomenon by delineating the process which causes it; a scientific theory generates predictions that can be falsified by the observation of an experiment.C1-0) Theories are more likely to be true when valid experiments do not falsify them; when they successfully predict observations.
* Note that a theory is still called a theory, even when confirmed by valid experiment hundreds or millions of times, because P1-0 does not hold as a logical truth. Note also that you trust your lungs to breathe primarily due to P1-0.

P1-1) Fossils are remnants of organisms [1].P2-1) Fossils formed across the last 3.8 billion years [2] as determined by our ability to date them within a substantial degree of accuracy [3].
* We can also date some types of fossils and rock absolutely with raioisotope dating [16][17][18].C1-1) Organisms have been on earth for at least 3.8 billion years and we know roughly when many types of them lived.P3-1) Fossils show specific groups living at specific times; with no fossils of humans, e.g., forming 3.8 billion years ago, and fossils of e.g. dinosaurs which are no longer extant today [2].C2-1) Evolution, the changing and growing complexity of the form of life on earth, as well as vast extinction of life, has occurred over the last 3.8 billion years.
* Note that at this point I have made no conclusions about how evolution has happened.

P1-2) Organisms reproduce themselves using their genetic coding, usually DNA [4][5].P2-2) Reproduction of DNA (and RNA) molecules in biological systems often leads to small mutations or changes in the DNA molecule [6].P3-2) Changes in DNA can lead to changes in protein structure [6].
* This premise is often referred to as part of the "central dogma" of biology; that DNA is ultimately translated into amino acid sequences.
* While "dogma" may sound like a strong term, we have actually synthesized DNA from simple compounds and given it to bacteria--who then use that DNA [7].
* It is further standard practice to give bacterial cells particular DNA sequences to have them produce the protein encoded by that DNA [8].C1-2) When organisms reproduce, sometimes mutations occur and lead offspring to have slightly different traits than the parent.
* This is partly an explanation of microevolution--note that bacteria can evolve both without the creation of 'new' genetic information [9] and due to mutations that occur during recombination and DNA copying [10].

P1-3) If an organism does not reproduce itself, it will eventually die and its genetic information will not be expressed.
* I think this follows deductively.C1-3) If a mutation does not help an organism reproduce, there will not be any pressure for that change in genetic information to promulgate.
* This is microevolution by natural selection. We see it all the time in antibiotic-resistant bacteria.

P1-4) Reproduction itself is governed by the expression of DNA.P2-4) Two populations of organisms that do not reproduce using one another's genetic material are of different species.C1-4) Species can diverge due to the accumulation of gradual mutations.
* This has been explored on a genetic level for past eukaryotic species divergence events [11][12].
* This has been observed in the present tense for bacteria [13].C2-4) Species can diverge due to reproductive pressure (from C1-3).
* This has been specifically observed in the present tense in many types of organism [14].
* This is the theory of evolution by natural selection.

Inferring using this with respect to the fossil record, we can further say:

C3-4) Evolution in the past can be explained as a consequence of species divergence due to reproductive pressure.

Obviously there's a lot more to explain; specific events that are shown by the fossil record still need to be explained. For example, why is it that change seems to occur sporadically, instead of all the time? For this particular point, there is a lot of evidence that genes are relatively stable without reproductive pressure; basically, the species under no pressure will only "wobble" genetically, on average staying the same [15]. In fact the general view is that one would only expect change when reproductive pressure is in play; that punctuated equilibrium is unsurprising. (There's also the interesting application of this theory to our own species.) However, I think this discussion would be best suited to focus on disagreements with the above argument; more detailed applications can be discussed if the basic argument is ever finished.

First let us provide a specific definition to the theory of "Natural Selection" before trying to apply it to a fossil record or confusing it with what is known about the process of genetic mutability and transference.

Charles Darwin is the originator of the theory of natural selection which has its premise based on aspects of animal husbandry were animals of the same species are bred in order to produce more desirable and advantageous traits. Horses, for instance, would be bred for specific utility: race horses for racing, pack horses for carrying and plow horses for plowing. By this example we must understand that Darwin's original theory, based on the primitive observations at the time has transformed from his original concept into the completely different definition of today. Before providing criticisms or rebuttals to the overall theory we must understand what the difference is between the classic and the modern representations of natural selection and the reasons for that metamorphosis.

Charles Lyell laid the groundwork for Darwin's theory through his observations of geology and his theory of "uniformatarianism" which fundamentally stated that the earth is very old and transformed by current observable phenomenon, volcanoes and earthquakes. So Darwin's theory had to fit with that concept of a very old earth.

We have to understand that Darwin, although he provides limited observations for his theory, was very much motivated by his own reasoning and the works and observations of others in his day. I mention this so that we can understand that Darwin really did not have any real empirical evidence for his theory and that it is basically a thought exercise for him.

In reality it can be argued that Darwin actually got the impetus to publish his seminal work "Origin of Species" as a result of reading a paper written by naturalist Alfred Russel Wallace. Not to give credit to Russel, but only to invite inquiry into the evolution of evolution theory.

The four main parts of Darwin's theory;

1. Organisms have changed over time, and the ones living today are different from those that lived in the past. Furthermore, many organisms that once lived are now extinct. The world is not constant, but changing. The fossil record provided ample evidence for this view.
2. All organisms are derived from common ancestors by a process of branching. Over time, populations split into different species, which are related because they are descended from a common ancestor. Thus, if one goes far enough back in time, any pair of organisms has a common ancestor. This explained the similarities of organisms that were classified together -- they were similar because of shared traits inherited from their common ancestor. It also explained why similar species tended to occur in the same geographic region.
3. Change is gradual and slow, taking place over a long time. This was supported by the fossil record, and was consistent with the fact that no naturalist had observed the sudden appearance of a new species.
4. The mechanism of evolutionary change was natural selection. This was the most important and revolutionary part of Darwin's theory, and it deserves to be considered in greater detail.

*One of the prime motives for all species is to reproduce and survive. When species do this they tend to produce more offspring than the environment can support.
*The lack of resources to nourish these individuals places pressure on the size of the species population, and the lack of resources means increased competition and as a consequence, some organisms will not survive.
*The organisms who die as a consequence of this competition were not totally random, Darwin found that those organisms more suited to their environment were more likely to survive.
*This resulted in the well known phrase survival of the fittest, where the organisms most suited to their environment had more chance of survival if the species falls upon hard times. (This phrase if often associated with Darwin, though on closer inspection Herbert Spencer puts the phrase in a more accurate historical context.)
*Those organisms who are better suited to their environment exhibit desirable characteristics.

Consider that Darwin had no idea of inherited traits and had no clue of genes as the driver of change. In fact Darwin actually regretted using the term "Natural Selection", preferring "Natural Preservation"

As we will see the concept of Natural Selection had to be modified due to the discovery of inherited traits and subsequently "genes".

Last edited by Juice on October 15th, 2009, 8:59 pm, edited 1 time in total.

When everyone looks to better their own future then the future will be better for everyone.

Juice wrote:First let us provide a specific definition to the theory of "Natural Selection" before trying to apply it to a fossil record or confusing it with what is known about the process of genetic mutability and transference.

I distinguished it; it is (P1-3) and (C1-3)--or the 3rd argument. The claims from the fossil record (1st argument) and DNA behavior (2nd argument) do not derive anything from the 3rd argument about natural selection.

Juice wrote:The four main parts of Darwin's theory;

I'm not really sure how this relates to the modern theory's validity as a scientific explanation. Maybe I'll understand once you draw conclusions from it.

To be honest there is so much history in natural history that it is indeed difficult to know where to start. Suffice it to say that an in depth study of the history of the science which led to Darwin's theory could occupy a man for a lifetime. So while on this topic it would be interesting and helpful if others could supply clarification or insight to points made or not. In order for us, the layman but the interested, to make a poignant determination of the validity of Darwinism we must take the time to understand the history. The rational for this methodology is so we can re-explore and rethink what we think we know.

Let's put Darwin's theory as simply as possible aside from simply using the term "CHANGE";

Classical;
Evolution did occur; Evolutionary change was gradual, requiring thousands to millions of years; The primary mechanism for evolution was a process called natural selection (determined by an organism's ability to adapt to its environment); The millions of species alive today arose from a single original life form through a branching process called "specialization."

The process by which individuals’ inherited needs and abilities are more or less closely matched to resources available in their environment, giving those with greater "fitness" a better chance of survival and reproduction.

Illustrations of the Action of Natural Selection "Origin of Species" chap 4-In order to make it clear how, as I believe, natural selection acts, I must beg permission to give one or two imaginary illustrations.

This is an extremely intricate subject. A large amount of inheritable and diversified variability is favourable, but I believe mere individual differences suffice for the work. A large number of individuals, by giving a better chance for the appearance within any given period of profitable variations, will compensate for a lesser amount of variability in each individual, and is, I believe, an extremely important element of success. Though nature grants vast periods of time for the work of natural selection, she does not grant an indefinite period; for as all organic beings are striving, it may be said, to seize on each place in the economy of nature, if any one species does not become modified and improved in a corresponding degree with its competitors, it will soon be exterminated.

I point out the above mentioned abstracts from Darwin's book in order to illustrate that Darwin based his theory primarily on speculation and a large dose of imagination.

The use of the term "specialization" is important since we must extrapolate what Darwin meant as it is unclear in his writings. But we can either surmise that Darwin meant, on a small scale, specialized organs of traits, or on a larger scale traits which allowed a particular species to be better adapted to an environment than others. I tend towards the later since this is the gist of Darwin's argument in that chapter.

We can understand that Darwin saw more complexity in the biosphere as a whole and did not concentrate, as yet, on individual and separate structures let alone the cell. Darwin never discusses origin of life, his whole work is an attempt to answer origin of species.

The modern theory of evolution is a sort of combination of Darwinism and Mendelian science.

When everyone looks to better their own future then the future will be better for everyone.

What made Darwin's theory scientifically useful is that it could be tested in an experimental setting. As I made my case above, I showed that we have proven evolution by natural selection occurs in bacteria and eukaryotes. Once this has been done, it makes plenty of sense to extrapolate the experimental case to historical cases where the same results, e.g. species divergence, came about under similar conditions, e.g. reproductive pressure.

In fact even Darwin attempted this in part (although obviously not to the mechanistic level of genetics). That's what his birds were all about; showing how it happens in a controlled environment, and then extrapolating to explain history.

Hello Alun, I haven't kept up with the literature re: natural selection but I have a question for you:

"When organisms reproduce, sometimes mutations occur and lead offspring to have slightly different traits than the parent."

Isn't there an unexplained discrepency between the rate at which favorable and reproducible mutations have been observed to occur in nature - very rarely as I understand it - and the wide divergence and variety of life that we see on Earth? Thank you.

"We do not see things as they are; we see things as we are." - Anaïs Nin

Felix, that's a fairly difficult question to answer, and definitely not as generally applicable as it sounds. A mutation can be as small a change as one almost unnoticeable amino acid in one protein, or it can be the amino acid in the active site of a protein that has a cascading effect on other proteins. The effect of a given mutation depends heavily on where it occurs, which in turn depends heavily on the organism involved.

On top of that, a mutation also doesn't have to be so simple; it could, for example, be the movement of a whole segment of a gene sequence into another. The rates of different types of mutations depend on the organism and even the area of the genome. Therefore any bald-faced claims about the universal likelihood of a beneficial mutation are virtually impossible to justify. There simply is not that kind of correlation across all the genes of all life on earth.

This article (pdf) is a meta-analysis, and essentially concludes that we do not yet know how often beneficial mutations occur even in simpler species such as fruit flies.

However, I do not think this really undermines the picture. The fact is that while it is very hard for us to look at every mutation in every organism in a population, we can watch organisms change in the direction of fitness, as I referenced in the OP, and we can watch the way a beneficial mutation spreads through a population in contrast to a non-beneficial mutation. We can then apply the patterns we see in evolution from experiments to the evolution that is shown in the fossil record; both of these, in general, correlate with what we expect of natural selection.

Great post, Alun! I think you've done a great job summarizing the facts and reasoning of evolution--particularly by laying it out in a logical format that clearly identifies the premises and conclusions. For those who are skeptical about aspects of the theory of evolution or the facts of evolution or who just have questions about it, they can specify precisely which premises they doubt or which logical inferences they think are invalid. This will avoid misunderstandings, straw-man arguments and "talking past each other."

Even though you have laid the groundwork for a productive discussion, I unfortunately already believe all the premises you posted and find your logic to be valid.

Belatedly: Thanks Scott. I keep hoping someone will drop in and challenge me to make the argument stronger. I suppose I could add a segment about the probability of genetic mutations and natural selection of actually producing the trends seen in history, but then I worry I'll get into too many competing scientific theories (how important is genetic drift, deleterious mutation vs. copying mutation etc., geographical isolation vs. ecological divergence, etc. etc.).

Also, I think there's work to be done in the pure philosophy of science part of the argument (which right now is just one premise), but it's hard to see where with nobody throwing questions at me.

Those from African decent are most apt to carry one of the two Sickle Cell Anemia mutations, because the prevalence of malaria in the region, gave those with one or the other mutation, an increased survival advantage.

Wikipedia explains:

because in areas where malaria is common, there is a survival value in carrying only a single sickle-cell gene (sickle cell trait).[3] Those with only one of the two alleles of the sickle-cell disease are more resistant to malaria, since the infestation of the malaria plasmodium is halted by the sickling of the cells which it infests.

Alun wrote:Reasons Behind the Theory of Evolution by Natural Selection

Hi Alun!

Your wish has come true in that I as a challenger in Love of both creation and evolution has just dropped in!:)

First of all, the answer as to the reasons behind the TOE by Natural Selection, as mentioned in the title of your thread, is supplied by Aldous Huxley himself:

"I had motive for not wanting the world to have a meaning; consequently assumed that it had none, and was able without any difficulty to find satisfying reasons for this assumption.

The philosopher who finds no meaning in the world is not concerned exclusively with a problem in pure metaphysics, he is also concerned to prove that there is no valid reason why he personally should not do as he wants to do, or why his friends should not seize political power and govern in the way that they find most advantageous to themselves.

For myself, the philosophy of meaninglessness was essentially an instrument of liberation, sexual and political."
Aldous Huxley, Ends and Means.
bolds & underline by ape

This statement by AH undermines and is seen to undermine and would seem to undermine the basis of what you say is "the basic premise of empirical inductive reasoning, [which] is a key to the scientific method in general."

Belinda wrote:Do you agree that there is no scientific proof that intelligence is not a universal quality of which intelligent thoughts, word and deeds are particular instances?

To my knowledge, science does not purport to prove anything metaphysically (universally), much less prove the lack of anything metaphysically. So yes, I agree that science does not aim to rule out souls, gods, or some higher calling behind intelligence.

However, I do think the above argument lays groundwork to rule out claims that metaphysical explanations are necessary--we are perfectly capable of explaining empirical events without using non-empirical basis arguments. That doesn't mean we shouldn't believe in God, for example, but it does mean we shouldn't think that there are empirical reasons that rationally require us to accept that God exists.

*******

ape wrote:Huxley: "I had motive for not wanting the world to have a meaning; consequently assumed that it had none, and was able without any difficulty to find satisfying reasons for this assumption."

This is indeed a motive that some people have for accepting the theory of evolution by natural selection. However, I am trying to present objective, empirical reasons to accept the theory--I want to avoid letting my subjective bias cloud the issue. As such, even someone who does not have a motive like Huxley would have to accept the evidence I present (if it is really valid)--otherwise, they'd have to dispense with the reasoning I use or contradict themselves.

Aldous Huxley is not using the scientific method by employing such a motive, or at least not what any scientists I know of would call the scientific method.

As a side note, I do think there is objective/real/universal quality/meaning; hence I certainly don't have Huxley's bias here.

ape wrote:Huxley: "I had motive for not wanting the world to have a meaning; consequently assumed that it had none, and was able without any difficulty to find satisfying reasons for this assumption."

This is indeed a motive that some people have for accepting the theory of evolution by natural selection.

Thanx for the admission.
But Alun, it is a lot more than 'some,' more likely 'most' if not 'all.'

"Any suppression which undermines and destroys that very foundation on which scientific methodology and research was erected, evolutionist or otherwise, cannot and must not be allowed to flourish ...
It is a confrontation between scientific objectivity and ingrained prejudice - between logic and emotion - between fact and fiction ...
In the final analysis, objective scientific logic has to prevail - no matter what the final result is - no matter how many time-honoured idols have to be discarded in the process ...
After all, it is not the duty of science to defend the theory of evolution and stick by it to the bitter end -no matter what illogical and unsupported conclusions it offers ...
If in the process of impartial scientific logic, they find that creation by outside intelligence is the solution to our quandary, then Lets cut the umbilical chord that tied us down to Darwin for such a long time. It is choking us and holding us back ... Every single concept advanced by the theory of evolution (and amended thereafter) is imaginary as it is not supported by the scientifically established probability concepts.Darwin was wrong... The theory of evolution may be the worst mistake made in science."
I L Cohen, Darwin Was Wrong - A Study in Probabilities PO Box 231, Greenvale, New York 11548: New Research Publications, Inc. pp 6-8, 209-210, 214-215. I.L.Cohen, Member of the New York Academy of Sciences and Officer of the Archaeological Institute of America.

Alun wrote:
As such, even someone who does not have a motive like Huxley would have to accept the evidence I present (if it is really valid)--otherwise, they'd have to dispense with the reasoning I use or contradict themselves.

Aldous Huxley is not using the scientific method by employing such a motive, or at least not what any scientists I know of would call the scientific method.

Exactly!

Alun wrote:
As a side note, I do think there is objective/real/universal quality/meaning; hence I certainly don't have Huxley's bias here.

Great!

But Alun, do you have any biases or prejudices?

Do you love and respect Huxley as prejudiced and as a prejudiced witness?

Do you love and respect yourself as biased and as unbiased?

Do you have equal Love and Respect for both creation and evolution?

Do you love yourself as both creationist and evolutionist, as both intelligent designer and its opposite?

Do you love yourself as right and as wrong?

Do you love yourself as God and as no God?

Here is why that is important:

"What has perhaps been overlooked [due to irrational Hatred of the irrational and etc] is the irrational, the inconsistent, the droll, even the insane, which nature, inexhaustibly operative, implants into the individual, seemingly for her own amusement. These things are singled out only in the crucible of one's own mind."
Albert Einstein

Wd you be willing to give up the TOE if proved wrong?

Wd you at least give creationsism an equal hearing even now before proved right or wrong?

'The British scientist, J.D. Bernal, emphasized the problem at hand, by suggesting that the scenario of a single molecule of DNA, created by chance, '... generating the rest of life was put forward with slightly less plausibility than that of Adam and Eve in the Garden.'
DICKERSON, R.E..
(September, 1978) Chemical Evolution and The Origin of Life. Scientific American, p.73